Francesco Napolitano
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/gep2pep |
| Branch: master |
| Last Commit: 0782762 |
| Last Changed Date: 2019-03-30 19:16:16 -0400 (Sat, 30 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:19:29 -0400 (Tue, 09 Apr 2019).
| Package 662/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gep2pep 1.3.1 Francesco Napolitano
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: gep2pep |
| Version: 1.3.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gep2pep_1.3.1.tar.gz |
| StartedAt: 2019-04-09 02:20:31 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:23:29 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 178.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gep2pep.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gep2pep_1.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/gep2pep.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gep2pep/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gep2pep’ version ‘1.3.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘gep2pep’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
gep2pep.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gep2pep ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘gep2pep’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gep2pep)
gep2pep.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(gep2pep)
>
> test_check("gep2pep")
Chunk 1 of 2, 519 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 665 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 538 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 691 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 549 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 685 bytes (current file size: 12.3 Kb)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 163 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
18.310 1.655 20.253
gep2pep.Rcheck/gep2pep-Ex.timings
| name | user | system | elapsed | |
| CategorizedCollection | 0.254 | 0.032 | 0.288 | |
| CondSEA | 1.438 | 0.264 | 1.718 | |
| PathSEA | 1.167 | 0.135 | 1.310 | |
| addSingleGeneSets | 1.040 | 0.090 | 1.231 | |
| as.CategorizedCollection | 0.589 | 0.078 | 0.670 | |
| buildPEPs | 0.870 | 0.104 | 0.985 | |
| checkRepository | 0.331 | 0.054 | 0.389 | |
| clearCache | 1.057 | 0.136 | 1.214 | |
| createMergedRepository | 0.929 | 0.154 | 1.091 | |
| createRepository | 0.266 | 0.043 | 0.314 | |
| exportSEA | 0.818 | 0.100 | 0.924 | |
| gene2pathways | 0.299 | 0.051 | 0.353 | |
| getCollections | 0.254 | 0.055 | 0.313 | |
| getDetails | 0.811 | 0.087 | 0.915 | |
| getResults | 0.802 | 0.088 | 0.898 | |
| importFromRawMode | 0.868 | 0.087 | 0.960 | |
| importMSigDB.xml | 0.215 | 0.040 | 0.257 | |
| loadCollection | 0.242 | 0.045 | 0.291 | |
| loadESmatrix | 0.731 | 0.095 | 0.832 | |
| loadPVmatrix | 0.700 | 0.091 | 0.802 | |
| loadSampleGEP | 0.002 | 0.001 | 0.003 | |
| loadSamplePWS | 0.002 | 0.001 | 0.002 | |
| makeCollectionIDs | 0.061 | 0.001 | 0.061 | |
| openRepository | 0.242 | 0.045 | 0.290 | |
| setId2setName | 0.079 | 0.001 | 0.080 | |